{"id":"https://openalex.org/W2951837466","doi":"https://doi.org/10.1093/bioinformatics/btz497","title":"Positive multistate protein design","display_name":"Positive multistate protein design","publication_year":2019,"publication_date":"2019-06-11","ids":{"openalex":"https://openalex.org/W2951837466","doi":"https://doi.org/10.1093/bioinformatics/btz497","mag":"2951837466","pmid":"https://pubmed.ncbi.nlm.nih.gov/31199465"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz497","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz497","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.inrae.fr/hal-02625007","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038835179","display_name":"Jelena Vu\u010dini\u0107","orcid":"https://orcid.org/0000-0002-3088-9301"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210110888","display_name":"Toulouse Biotechnology Institute, Bio & Chemical Engineering","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210110888"]},{"id":"https://openalex.org/I4210154939","display_name":"G\u00e9n\u00e9tique Physiologie et Syst\u00e8mes d'Elevage","ror":"https://ror.org/04gg6ne93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I205747304","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210154939"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Jelena Vucinic","raw_affiliation_strings":["LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I17866349","https://openalex.org/I4210110888"]},{"raw_affiliation_string":"MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France","institution_ids":["https://openalex.org/I17866349","https://openalex.org/I4210154939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005612122","display_name":"David Simoncini","orcid":"https://orcid.org/0000-0002-3772-5473"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I134560555","display_name":"Universit\u00e9 Toulouse III - Paul Sabatier","ror":"https://ror.org/02v6kpv12","country_code":"FR","type":"education","lineage":["https://openalex.org/I134560555"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I3131550300","display_name":"Universit\u00e9 Toulouse-I-Capitole","ror":"https://ror.org/0443n9e75","country_code":"FR","type":"education","lineage":["https://openalex.org/I3131550300"]},{"id":"https://openalex.org/I4210110888","display_name":"Toulouse Biotechnology Institute, Bio & Chemical Engineering","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210110888"]},{"id":"https://openalex.org/I4210119061","display_name":"Institut de Recherche en Informatique de Toulouse","ror":"https://ror.org/01rx4qw44","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I205747304","https://openalex.org/I4210119061","https://openalex.org/I4210152422","https://openalex.org/I4405258862","https://openalex.org/I4405259414"]},{"id":"https://openalex.org/I4210152422","display_name":"Universit\u00e9 Toulouse - Jean Jaur\u00e8s","ror":"https://ror.org/04ezk3x31","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210152422"]},{"id":"https://openalex.org/I4210160189","display_name":"Institut Polytechnique de Bordeaux","ror":"https://ror.org/054qv7y42","country_code":"FR","type":"education","lineage":["https://openalex.org/I4210160189"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"David Simoncini","raw_affiliation_strings":["IRIT UMR 5505-CNRS, Universit\u00e9 de Toulouse , 31042 Cedex 9, France","LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IRIT UMR 5505-CNRS, Universit\u00e9 de Toulouse , 31042 Cedex 9, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I134560555","https://openalex.org/I17866349","https://openalex.org/I3131550300","https://openalex.org/I4210119061","https://openalex.org/I4210152422","https://openalex.org/I4210160189"]},{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I17866349","https://openalex.org/I4210110888"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067543527","display_name":"Manon Ruffini","orcid":null},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210110888","display_name":"Toulouse Biotechnology Institute, Bio & Chemical Engineering","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210110888"]},{"id":"https://openalex.org/I4210154939","display_name":"G\u00e9n\u00e9tique Physiologie et Syst\u00e8mes d'Elevage","ror":"https://ror.org/04gg6ne93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I205747304","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210154939"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Manon Ruffini","raw_affiliation_strings":["LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I17866349","https://openalex.org/I4210110888"]},{"raw_affiliation_string":"MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France","institution_ids":["https://openalex.org/I17866349","https://openalex.org/I4210154939"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053009384","display_name":"Sophie Barbe","orcid":"https://orcid.org/0000-0003-2581-5022"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210110888","display_name":"Toulouse Biotechnology Institute, Bio & Chemical Engineering","ror":"https://ror.org/01yypjb30","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I196454796","https://openalex.org/I4210088668","https://openalex.org/I4210110888"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Sophie Barbe","raw_affiliation_strings":["LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"LISBP, Universit\u00e9 de Toulouse, CNRS, INRA, INSA , 31400 Toulouse, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I17866349","https://openalex.org/I4210110888"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080878843","display_name":"Thomas Schiex","orcid":"https://orcid.org/0000-0001-6049-3415"},"institutions":[{"id":"https://openalex.org/I17866349","display_name":"Universit\u00e9 F\u00e9d\u00e9rale de Toulouse Midi-Pyr\u00e9n\u00e9es","ror":"https://ror.org/004raaa70","country_code":"FR","type":"education","lineage":["https://openalex.org/I17866349"]},{"id":"https://openalex.org/I4210154939","display_name":"G\u00e9n\u00e9tique Physiologie et Syst\u00e8mes d'Elevage","ror":"https://ror.org/04gg6ne93","country_code":"FR","type":"facility","lineage":["https://openalex.org/I176063091","https://openalex.org/I205747304","https://openalex.org/I4210088668","https://openalex.org/I4210117091","https://openalex.org/I4210154939"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Thomas Schiex","raw_affiliation_strings":["MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MIAT, Universit\u00e9 de Toulouse , INRA, 31326 Castanet-Tolosan Cedex, France","institution_ids":["https://openalex.org/I17866349","https://openalex.org/I4210154939"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5053009384","https://openalex.org/A5080878843"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I17866349","https://openalex.org/I4210110888","https://openalex.org/I4210154939"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0629,"has_fulltext":false,"cited_by_count":27,"citation_normalized_percentile":{"value":0.76009999,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"36","issue":"1","first_page":"122","last_page":"130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9251000285148621,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.9251000285148621,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11162","display_name":"Enzyme Structure and Function","score":0.00860000029206276,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.00570000009611249,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5889265537261963},{"id":"https://openalex.org/keywords/protein-design","display_name":"Protein design","score":0.5093585252761841},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32592523097991943},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.25874704122543335},{"id":"https://openalex.org/keywords/protein-structure","display_name":"Protein structure","score":0.196183979511261},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18471625447273254},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.17036154866218567}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5889265537261963},{"id":"https://openalex.org/C152769699","wikidata":"https://www.wikidata.org/wiki/Q410814","display_name":"Protein design","level":3,"score":0.5093585252761841},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32592523097991943},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.25874704122543335},{"id":"https://openalex.org/C47701112","wikidata":"https://www.wikidata.org/wiki/Q735188","display_name":"Protein structure","level":2,"score":0.196183979511261},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18471625447273254},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.17036154866218567}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D015202","descriptor_name":"Protein Engineering","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btz497","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz497","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31199465","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31199465","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:HAL:hal-02625007v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-02625007","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://academic.oup.com/bioinformatics","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-02625007v1","is_oa":true,"landing_page_url":"https://hal.inrae.fr/hal-02625007","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"https://academic.oup.com/bioinformatics","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/7","display_name":"Affordable and clean energy","score":0.8299999833106995}],"awards":[{"id":"https://openalex.org/G1938070154","display_name":"Artificial and Natural Intelligence Toulouse Institute","funder_award_id":"ANR-19-P3IA-0004","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G5140280351","display_name":"Decomposition of Graphical Models","funder_award_id":"ANR-16-CE40-0028","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W47957325","https://openalex.org/W1988443389","https://openalex.org/W1990759986","https://openalex.org/W1991917050","https://openalex.org/W1996576490","https://openalex.org/W2002452896","https://openalex.org/W2011658408","https://openalex.org/W2026461419","https://openalex.org/W2035056536","https://openalex.org/W2046994420","https://openalex.org/W2054467356","https://openalex.org/W2065251436","https://openalex.org/W2082527422","https://openalex.org/W2106775540","https://openalex.org/W2110281506","https://openalex.org/W2130479394","https://openalex.org/W2140588153","https://openalex.org/W2141795045","https://openalex.org/W2151581834","https://openalex.org/W2155432846","https://openalex.org/W2164958220","https://openalex.org/W2168510900","https://openalex.org/W2173184980","https://openalex.org/W2252678535","https://openalex.org/W2328911273","https://openalex.org/W2342178758","https://openalex.org/W2558409629","https://openalex.org/W2606439133","https://openalex.org/W2627077205","https://openalex.org/W2809695261","https://openalex.org/W2891007938","https://openalex.org/W2900778631","https://openalex.org/W2952146947","https://openalex.org/W6633670702"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829","https://openalex.org/W2952785685"],"abstract_inverted_index":{"MOTIVATION:":[0],"Structure-based":[1],"computational":[2,69,151],"protein":[3,15,112],"design":[4,57,152],"(CPD)":[5],"plays":[6],"a":[7,32,38,45,50],"critical":[8],"role":[9],"in":[10,92],"advancing":[11],"the":[12,93,122,137,142],"field":[13],"of":[14,76,108,156],"engineering.":[16],"Using":[17],"an":[18],"all-atom":[19],"energy":[20,139],"function,":[21],"CPD":[22],"tries":[23],"to":[24,61,80,103,121,126],"identify":[25,104],"amino":[26],"acid":[27],"sequences":[28,107,119],"that":[29,136],"fold":[30],"into":[31],"target":[33],"structure":[34],"and":[35,89,115,130,158],"ultimately":[36],"perform":[37],"desired":[39],"function.":[40],"The":[41],"usual":[42],"approach":[43],"considers":[44],"single":[46],"rigid":[47],"backbone":[48,54,64],"as":[49,174],"target,":[51],"which":[52],"ignores":[53],"flexibility.":[55],"Multistate":[56,96],"(MSD)":[58],"allows":[59],"instead":[60],"consider":[62],"several":[63],"states":[65],"simultaneously,":[66],"defining":[67],"challenging":[68],"problems.":[70],"RESULTS:":[71],"We":[72],"introduce":[73],"efficient":[74],"reductions":[75],"positive":[77,109],"MSD":[78,123,161],"problems":[79,114,162],"Cost":[81],"Function":[82],"Networks":[83],"with":[84,163,167],"two":[85],"different":[86],"fitness":[87,140],"definitions":[88],"implement":[90],"them":[91],"Pompd":[94,100],"(Positive":[95],"Protein":[97],"design)":[98],"software.":[99],"is":[101],"able":[102],"guaranteed":[105,150,168],"optimal":[106],"multistate":[110],"full":[111],"redesign":[113],"exhaustively":[116],"enumerate":[117],"suboptimal":[118],"close":[120],"optimum.":[124],"Applied":[125],"nuclear":[127],"magnetic":[128],"resonance":[129],"back-rubbed":[131],"X-ray":[132],"structures,":[133],"we":[134],"observe":[135],"average":[138],"provides":[141],"best":[143],"sequence":[144],"recovery.":[145],"Our":[146],"method":[147],"outperforms":[148],"state-of-the-art":[149],"approaches":[153],"by":[154],"orders":[155],"magnitudes":[157],"can":[159],"solve":[160],"sizes":[164],"previously":[165],"unreachable":[166],"algorithms.":[169],"AVAILABILITY":[170],"AND":[171],"IMPLEMENTATION:":[172],"https://forgemia.inra.fr/thomas.schiex/pompd":[173],"documented":[175],"Open":[176],"Source.":[177],"SUPPLEMENTARY":[178],"INFORMATION:":[179],"Supplementary":[180],"data":[181],"are":[182],"available":[183],"at":[184],"Bioinformatics":[185],"online.":[186]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":8}],"updated_date":"2026-07-31T08:31:51.225901","created_date":"2025-10-10T00:00:00"}
